Healthier Chocolate Chip Cookies

This is a recipe I posted several years ago, but I pulled it out last week and made a batch. I find the process of making chocolate chip cookies comforting, maybe because it was one of the first baked goods I made on my own at a kid. I figured I’d re-share the recipe again, since maybe you could use that kind of comfort, too. 

There are weeks when my kids do so much baking, I wonder if I’m not living in a tiny cookie factory with amateur bakers at the helm. It makes me happy that they want to experiment in the kitchen, but too many sugary treats isn’t good for anyone. This is why I’m forever tinkering with traditional recipes to make them just a bit more nutritious, such as these healthier chocolate chip cookies.

I’m guessing cookies might be popular around your house too, so I thought I’d share my tips on tailoring baked goods for the better. With just a handful of swaps and substitutions in these chocolate chip cookies, for example, you’ve got a sweet treat that’s lower in sugar and saturated fat and higher in fiber and nutrients. It’s not health food, that’s not what cookies are for. It’s a treat, but one that’s less likely to give you a sugar high followed by an energy slump. With that in mind, here are some of my standard baking makeovers:

Healthier Chocolate Chip Cookies with glasses of milk

How to Make Healthier Chocolate Chip Cookies

1. Use whole-grain flour

Instead of relying on white flour, which loses fiber and nutrients in the processing, experiment with whole-wheat flour. You can pretty seamlessly swap out at least half the all-purpose flour for whole wheat flour in most cookies. If you have whole-wheat pastry flour, that makes an even more seamless swap, since the flour is lighter in texture and flavor.

2. Add oats

Adding rolled oats can enhance a cookie both nutritionally and in terms of flavor and texture. You can add them whole, grind them in a blender or food processor, or buy oat flour to use in place of some of the white flour.

3. Use dark chocolate

The darker the chocolate, the higher the antioxidants and the lower the sugar. Some brands now make chips with upwards of 60 percent cacao. Alternatively, chop up a block of good quality dark chocolate to use in place of the chips.

4. Make butter better

Butter is part of what makes cookies so rich and satisfying, which is why you can likely get away with using a bit less than you might expect. You can also substitute some of the butter with a neutral oil such as organic canola to minimize saturated fat. Alternatively, try  try browning butter before adding it to the batter, which lends a pleasing, nutty flavor to the mix.

5. Work in nuts

Adding walnuts, peanuts, almonds, hazelnuts, and so forth brings crunch and texture to cookies, but also adds nourishment and healthy fats that can give cookies a little staying power. You can stir chopped nuts into your batter or nut flour to replace some of the all-purpose flour. Alternatively, make it yourself by pulverizing nuts in a blender or food processor.

6. Scale down the Sugar

Some form of sweetener, whether it’s white sugar, coconut, honey, or maple syrup is key for cookies. But you might be surprised that you can trim the amount without much of an impact on flavor or texture. This recipe, for instance, calls for 1/3 less sugar than standard cookies.

7. Downsize

Super sized cookies are a real show-stopper, but it’s wise to scale your cookies down. It’s tough to stop at just one, so smaller is often better.

Healthier Chocolate Chip Cookies on a sheet pan


If you’ve go kids who like to eat the dough, consider using pasteurized eggs, such as Safest Choice.

Looking for more healthy cookie inspiration? Check out these recipes.

Chocolate-Dipped Tahini Cookies

Double Ginger Molasses Rye Cookies

Cocoa Peanut Butter Whoopie Pies

Vegan Chocolate Chip Oatmeal Cookies by Pamela Salzman

Red Lentil Snack Cookies by Liz’s Healthy Table

Healthier Chocolate Chip Cookies on a sheet pan
3.5 from 4 votes

Healthier Whole-Grain Chocolate Chip Cookies

The Toll House classic gets a healthier chocolate chip cookie makeover here by calling for whole wheat, almond, and oat flour in place of standard white flour. It cuts the amount of butter in half, the sugar by a third, and uses antioxidant-rich dark chocolate in place of semi-sweet chocolate. The result is a delicious chocolate chip cookie that doesn't taste like it was shortchanged in the decadence department.
Course Dessert, Snack
Prep Time 20 minutes
Cook Time 10 minutes
Total Time 31 minutes
Servings 3 1/2 dozen cookies
Calories 84 kcal
Author katiemorford


  • 2/3 cup almond flour, spooned an leveled in the measuring cup
  • 2/3 cup oat flour, spooned and leveled in the measuring cup
  • 1 1/4 cups whole wheat pastry flour, spooned and leveled in the measuring cup (alternatively use whole-wheat or white whole-wheat
  • 3/4 teaspoon baking soda
  • 3/4 teaspoon baking powder
  • 1/2 teaspoon kosher salt
  • 1 stick butter (4 ounces), softened to room temperature
  • 1/2 cup firmly packed brown sugar
  • 1/2 cup granulated sugar
  • 2 teaspoons vanilla extract
  • 2 eggs (use pasteurized eggs such as Safest Choice if you want to eat the dough!)
  • 1 1/3 cups dark chocolate chips or about 8 ounces chopped dark chocolate


  1. Preheat oven to 350 degrees. Lightly grease or line baking sheets with parchment paper.
  2. Cream the butter, brown sugar, and granulated sugar with an electric mixture until light and creamy. about 2 minutes. Add the eggs and vanilla and continue to beat until light and smooth, another minute. 

  3. Add the almond flour, oat flour, whole-wheat pastry flour, baking soda, baking powder, and salt to the bowl with the butter. Use a fork to lightly mix the dry ingredients together. 

  4. Beat the ingredients together until creamy, 1 minute. Add the chocolate chps and beat to combine. 

  5. Arrange tablespoon-size balls of dough on baking sheets. Bake until the bottoms are lightly brown and you just start to see a hint of pale brown around the edges, about 10 minutes.

  6. Remove from the oven. Cool and store in an air-tight container.

Thank you to Safest Choice Eggs for sponsoring this post



05.28.2013 at 3:40 AM #

Sally Kuzemchak

Yum! These look great. I love adding oats to cookies–and I find that it makes the cookies much more filling, so I can be satisfied with just one (or two)! Pinning these now to try later. Thanks for the great recipe Katie.

05.28.2013 at 3:40 AM #


Thanks Sally. I agree…the grains, nuts, and eggs give cookies a foundation in something other than sugar, which is more sustaining.

05.28.2013 at 7:49 AM #

Heather Christo

These look seriously amazing!!

05.28.2013 at 2:09 PM #


great recipe. i like the healthy tweaks you made. it was just enough to make it healthy but still delicious!

05.28.2013 at 2:19 PM #


Just when I think I can’t love you anymore! I’m really excited to try these this summer!

05.28.2013 at 2:19 PM #



05.28.2013 at 5:07 PM #


I can’t wait to try these! Maybe even tonight…

05.28.2013 at 5:07 PM #


Must report back!

05.29.2013 at 4:04 AM #


Hi Katie

Thanks for your very informative blog. I’m gluten & dairy intolerant and always try to find ways baking stuff that I can eat.
Can you please tell me what a stick of butter means = weight? Sorry living in South Africa and butter / margerine is only available in 250 / 500gm.
many thanks

05.29.2013 at 4:04 AM #


Greetings to you South Africa! One stick of butter is equivalent to 113 grams or 4 ounces or 1/2 cup.

05.29.2013 at 10:05 AM #


What could I substitute for the almonds? How much more flour or oats could I add?

05.29.2013 at 10:05 AM #


You could add a different nut such as walnuts or pecans. If you don’t want to use nuts, I might add 1/2 cup of whole wheat pastry flour…but without trying it, can’t be sure of the result. Good luck!

05.30.2013 at 12:02 AM #

kim brady

I love makeovers! Can you tell me the difference between white whole wheat and whole wheat flour- I see them both at Trader Joe’s and curious as I usually stick with whole wheat pastry from Rainbow for baking. Also my mom once told me to swap out 1/2 cup wheat germ in baking to up the nutritional value would this work here- I like the way it gives waffles, breads and muffins a lightness but am not usually a cookie baker. Thanks Katie, my LO has recently discovered cookies so this will be a fun recipe to start with.

05.30.2013 at 12:02 AM #


Hi Kim…whole wheat white flour is a different variety than regular whole wheat with a milder flavor. I think it works well for baking and still has good nutritional value like other whole wheat. Worth trying.

05.30.2013 at 7:19 AM #


This cookie looks great wondering how many carbs are in one cookie. I count carbs.

05.30.2013 at 7:19 AM #


Hi there

I don’t run nutritional analyses on my recipes, but I know there are lots of apps and online resources available to do that.

05.30.2013 at 9:51 AM #


Are the top cookies the same as the bottom?I had cookies that looked like the top ones and they’re amazing!

05.30.2013 at 9:51 AM #


The top photo is the final version of the recipe.

08.14.2013 at 10:20 AM #


Katie, do you have any guidelines for how much sugar you can remove from a recipe before it effects texture and taste? Your guidelines here are excellent, but in addition to dropping the saturated fats and increasing the whole grains in my baked goods, I wonder sometimes if I could also reduce the sugar?

08.14.2013 at 10:20 AM #


I don’t have any specific guideline. I play around with lessening the sugar in recipes quite a bit but find it’s really a matter of trial and error. You are right, it affects both texture and sweetness, which is part of the challenge. Wish I could be more help.

10.01.2013 at 9:34 AM #

Maria in Tx

I made this, but used regular whole wheat flour and added a few tbs of flax. They didn’t flatten out, but instead stayed in balls. Tasty, but not sure I can pass them off to my kids as cookies 🙂

10.01.2013 at 9:34 AM #


Hi Maria, I find whole-wheat pastry flour is a little lighter and so has a result more similar to white flour in baking. You might also try the technique for making a prettier cookie I wrote about here since it involves flattening the cookies during the baking process. Just a thought.

10.10.2013 at 1:45 PM #


Hello, Great recipe! I have almond flour at home and I’m wondering if I can use that rather than grinding up almonds?
Thank you 🙂

10.10.2013 at 1:45 PM #


Hi Catherine

I haven’t made it with almond flour, but expect that it would work fine. The question would be how much almond flour because I didn’t measure how much ground almonds resulted after running them through the food processor. My guess is 3/4 cup of almonds would yield a bit more than that once ground up. Let me know how it goes.

09.06.2015 at 6:52 AM #


I am definitely gonna try this recipe tonight! Could you please tell for how long do these cookies last?

09.06.2015 at 6:52 AM #


Stored in an airtight container, they are best eaten within five days or so. You can also freeze both the dough and cookies, if you like.

07.14.2016 at 7:26 AM #


These were FANTASTIC! I don’t think I’ll go back to the old recipe when these are just as yummy (if not more) and healthier! I used walnuts instead of almonds (b/c I love walnuts). I think you can cut the sugar a little bit more without losing the sweetness but maybe it’s b/c I used semi-sweet chocolate chips. Substitutes I made: walnuts, white whole wheat flour, semi sweet chocolate chips (what I had).

07.14.2016 at 7:26 AM #


Terrific! That sort of comment makes my day. Thank you for sharing.

07.06.2018 at 2:00 PM #


Sorry, but, I lost attention at “one stick of butter”. I use applesauce for any fat in cookies or muffins, etc… And I soak a cup of REAL oatmeal, not quick or instant, in skim milk. At my house we can’t just eat just one, so I find it better to make things as fat free as possible. Though I know a person needs SOME fat, I am sure we manage to get enough, in other things we eat. I use dried cherries,raisins or cranberries to oamp up the flavor. I only use egg whites as each yolk is 5 grams of fat. And I use Splenda brown sugar. For chocolate muffins or cookies, then I throw in SOME dark chocolate chips. Using applesauce instead of butter, the product doesn’t brown as much, but, we would rather have several of these rather than feel guilty of having one of the ones loaded with fat. Just my opinion. I have used several of your other recipes, and we liked them, but this one is just too fattening for me.

07.06.2018 at 2:00 PM #


Hi Carla,

Thanks for chiming in. What works for one person may not work for another, which is sort of the beauty of home cooking…you can find what suits you best. Love your ideas for using applesauce and adding dark chocolate chips!


05.02.2020 at 10:20 AM #

Michael Stimpson

We recently used this recipe in our YouTube video comparing 3 chocolate chip recipes. This was our 1-star rated cookie recipe. We didn’t have very high expectations with such a low rating, but it turned out better than we expected! Thanks for sharing the recipe with us!

YT video:

05.09.2020 at 4:50 AM #

Kellie jobe

I’m guessing I could swap coconut flour for almond? Or just use more of the pastry flour? I have someone allergic to almonds.

05.09.2020 at 4:50 AM #


That would be a great swap.

05.19.2020 at 12:45 AM #


Love everything that includes dark chocolate. I’m also trying to switch to a healthier lifestyle and started to mine for healthy recipes like yours. Also, I started a training plan with SportMe run tracker app, and I managed to get rid of some pounds. Your blog posts are super inspiring for me in this phase, thanks!

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